see below
On Tue, Oct 6, 2015 at 1:28 AM, Sara Omar <sara.ibrahim.omar.gmail.com>
wrote:
> Dear all,
>
> I ran an MD simulation of a protein which has one non-standard amino-acid.
> I used MMPBSA.py to calculate the binding free energy (with pairwise
> residue decomposition). There were two observations that I did not
> understand:
> 1. What does the pairwise decomposition of a residue with itself mean? For
> example, what does the energy decomposition between Ser1 and Ser1 pair
> mean?
>
interactions between atoms that are both in Ser1.
> 2. The backbones of the non-standard amino acid had zero energy
> contribution. All the energy was that of the sidechain interactions. Why is
> that so?
>
the division into backbone and side chain is only done if Amber recognizes
the residue name. For nonstandard residues Amber has no way of know if this
division is appropriate (it might be a ligand or anything else). If you
want to add a new residue it is fairly straightforward to modify the code
> I would really appreciate your help and comments on this!
> Thank you!
>
> Kindest regards,
> Sara I Omar
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Received on Tue Oct 06 2015 - 04:00:03 PDT
